Thursday, May 13, 2010

Evolution v37.302

This blog is erroneous and I have retracted the offending section. Apologies for the false publicity.

two men say they’re Jesus one of them must be wrong—Dire Straits

Historian Stephen Brush points out that the origin of the solar system remains unsolved because, though textbooks will dogmatically present the current theory, in fact the “current” theory seems to be changing on a regular basis. All the more so for evolution, which seems to be pivoting at an ever increasing rate. Consider the origin of the complicated eukaryotes. Practically every permutation has been suggested on the basic model of an ancestor splitting three ways to give rise to bacteria, archaea and eukaryotes. Perhaps the archaea split off from the eukaryote lineage, or perhaps the bacteria split off from the archaea lineage. Perhaps the bacteria split off from the eukaryote lineage, or perhaps the archaea and bacteria lineages produced a fusion that led to eukaryotes. For being an undeniable fact, it’s amazing how little evolution fits the facts.

Recently however, it seemed that at least some of this ambiguity was finally resolved. That finicky eukaryote lineage was finally nailed down for good. There was no question about it, the eukaryotes arose from a unique fusion event between a lonesome bacteria and archaea. Here is what I wrote just a few months ago:

I wish I had a nickel for every statement of evolutionary certainty that later had to be dropped. Carl Zimmer’s recent piece on how eukaryotes are supposed to have evolved quotes Eugene Koonin as stating that “it is certain” that a long time ago, in a warm pond far far away, two cells (an archaea and a bacteria) symbiotically merged to form the first eukaryote. The rest, as they say, was history, as from that humble eukaryote sprung everything from the trilobite to the tyrannosaurus.

68 comments:

'I wish I had a nickel for every statement of evolutionary certainty that later had to be dropped' - surely you would have earned a lot more than one nickel by now? I would think you would be quite wealthy in fact!

'...the origin of the solar system remains unsolved...the “current” theory seems to be changing on a regular basis' - yep, sure does.

'...less than a year later, evolutionists have switched it round yet again' - yes, and this sort of thing happens time and time again.

I will happily bet you double or nothing of all the nickels you've earned so far and will amass in the future that in all such cases, the ultimate answer will be evolutionary science. Not a designer. Or a god. Or anything else but pure science.

Evolutionists try to outdo each other by seeing who can tell the tallest tale, to obtain funding and continue to make a living. For over 30 years now I have seen this going on with the descent of man from the ape like creatures story. Every couple of years or so the media hype announces this great fossil discovery that "finally closes the gap between man and apes" or, "will rewrite the descent of man from the apes". These stories end up being discarded in the garbage dump of evolutionary story telling a few months later without any media fuss. I find it amusing that even the foremost apostle of evolution, atheist Richard Dawkins, could not give Ben Stein an answer of how the first self replicating cell came to be through an evolutionary process. Pressed by Stein he literally admitted that he would rather believe in aliens planting life on earth than to believe in God. Obviously in his eyes these aliens evolved through some Darwinian process. Huh? Talk about a clown.

Cornelius Hunter: Now, less than a year later, evolutionists have switched it round yet again.

Um, no.

But first, let's consider that we are discussing the evolutionary origin of organisms from billions of years ago that left virtually no fossil evidence, and yet, we are able to make reasonable determinations concerning that history.

In any case, universal common descent is not inconsistent with symbiotic fusion events. The archaea and bacteria that are posited to form the primordial eukaryote themselves share a common ancestor.

From Theobald's paper: Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events.

I think I know the secret of evolutionary motivation. You are wrong. It has nothing to do with ideology. In the academic world it is publish or perish. What better job security than evolution. It doesn't matter what you publish. You can take one stand one day, then another the next. You can agree with someone on one day, and disagree the next. It is the perfect academic field. Actually, you could say that evolutionary sciences is extrememly well designed for the purpose of the scientific employment - 100% job security. No union has that benefit. :)

The crux of the matter is that "fact" of evolution itself is never questioned while its theories of how it actually happened are ever changing. Hyped certainities this year, fade into the mythology next year.

Perhaps the QUANITITY of half-baked conclusions are better than QUALITY of facts. A million half-facts equals a fact. Is that how it works?

I think evolutionists try to apply the theory of evolution to the process of science itself. They think that science is evolving. They try to make up random stories, and select the ones that sound best. Some alternative theories are discarded because they are thought to be extinct. But that is not how science works. Science is done by designing theories using logic.Evolution is like shell game. Each cup represents an evolutionary story. When you lift all of the cups at once you will notice not only there is no ball, but you have just been robbed (your tax money).

"So, am I right to say that you think the way science should be done is:(1) Take a stand (2) Stick with it

I really don't get what you think is supposed to happen through experimentation and research."

This is an example of the importance of the degree of variation. I am not saying that no change is good, or that some change is good. I am saying that with most scientific theories there is not the degree of change that we see in evolution. In fact, I would go further and say that there is an extreme amount of variation in the theory of evolution compared to other scientific theories. Take for example the human evolution narrative, or Darwin's three of life. Both change constantly.

Those crazy evolutionists! Always modifying their theory to fit new 'facts' and 'data'. It seems like the faster fields like genetics and paleontology yield new information, the faster they change their theory to 'accommodate' it. No telling what those yahoos will believe tomorrow when new data is presented.

As for me, I'm glad that *real science* is unchanging and immutable, no matter what new 'evidence' pops up.

Although sometimes I do feel sorry for the poor deluded chaps. After all, they don't have the answers to the origins of life already printed out for them in the KJV, do they Cornelius?

===== Cornelius Hunter: Now, less than a year later, evolutionists have switched it round yet again.

Um, no.=====

So the best fit model is not necessarily the right one?

====== But first, let's consider that we are discussing the evolutionary origin of organisms from billions of years ago that left virtually no fossil evidence, and yet, we are able to make reasonable determinations concerning that history.======

I didn't know that. And where are these "reasonable determinations." Obviously not in the Theobald paper which follows the usual circular logic of first assuming evolutionary premises and then finding that evolution is yet again the winner, despite the scientific absurdities.

======== In any case, universal common descent is not inconsistent with symbiotic fusion events. The archaea and bacteria that are posited to form the primordial eukaryote themselves share a common ancestor.========

But introducing the fusion event to create eukaryotes resulted in a poorer fit.

====== From Theobald's paper: Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events.======

But the data showed the fusion event is a weaker model. Aren't we following the data?

Cornelius: "Obviously not in the Theobald paper which follows the usual circular logic of first assuming evolutionary premises and then finding that evolution is yet again the winner,"

Paper: "...a sceptic who rejects the commonancestry of all life might nevertheless accept that universally conserved proteins have similar sequences and are ‘homologous’.... Here I report tests of the theory of UCA using model selectiontheory, without assuming that sequence similarity indicates a genealogical relationship."

Cornelius: But the data showed the fusion event is a weaker model. Aren't we following the data?

Paper: "...the endosymbiotic fusion hypotheses are nested within the class II hypotheses shown in Table 2. For nested hypotheses, the constrained versions necessarily have equal or lower likelihoods than the unconstrained versions."

NECESSARILY!That is, the constraint FORCES the scores to be only equal or lower. They can't score higher! It doesn't invalidate the model that they don't score higher.

"In terms of a fusion hypothesis for the origin of Eukarya, the data conclusivelysupport a UCA model in which Eukarya share an ancestor with Bacteria and another independently with Archaea, and in which Bacteria and Archaea are also genetically related independently ofEukarya (see Table 3)."

I think the first premise for this post by Dr. Hunter stems from a selective reading. Correct me if I'm wrong, but the paper CLEARLY does not reject endosymbiont theory. It finds support for a Universal common ancestor "irrespective of the presence of horizontal gene transfer andsymbiotic fusion events", and actually finds specific models supporting it.

The second premise, that science should never be wrong is hilarious to me, and seems to contradict Dr. Hunter's portrayal of it as a unbending religious dogma.

Seems to me that evolution is suffering from the very thing that Anthony Flew accused theists of in his story of the invisible gardener. Continually producing more and more ad hoc explanations for a belief.

CorneliusRobert is right. Theobald wasn't testing the fusion hypothesis. he was testing whether assuming the fusion hypothesis was true affected the likelihood of UCA. He found that it did not. bc the fusion hypotheses are nested, they mathematically can't be more likely than the non-fusion hypotheses. THus comparing the scores from the fusion vs non-fusion hypotheses is not meaningful; you have to examine each set of hypotheses independently. in short, yet another reading comprehension and statistics failure on this blog.

=====they mathematically can't be more likely than the non-fusion hypotheses.=====

I think you're confused, but not sure since it is not quite clear what you're saying in the first place. Bottom line is, different models can always have different likelihoods, one way or another, unless one of the models is simply the other model plus some additional DOFs (iow, a superset), in which case the superset model cannot have a lower likelihood.

=====Cornelius: "Obviously not in the Theobald paper which follows the usual circular logic of first assuming evolutionary premises and then finding that evolution is yet again the winner,"

Paper: "...a sceptic who rejects the common ancestry of all life might nevertheless accept that universally conserved proteins have similar sequences and are ‘homologous’.... Here I report tests of the theory of UCA using model selection theory, without assuming that sequence similarity indicates a genealogical relationship."=====

That wasn’t what I was referring to, but since you mention it, why, silly me. Just because the entire analysis is based on sequence alignment scores doesn’t really mean anything. Classic evolution-speak, written for and by evolutionists and signifying nothing.

Cornelius,I'm pointing out that the entire premise of your post is based on a faulty reading of the paper. THis paper does not say "...the fusion story is out and common descent is in." It says common descent is in whether or not the fusion story is in or out.

when you say "But introducing the fusion event to create eukaryotes resulted in a poorer fit" you are exposing the source of your confusion. the poorer fit is caused by the fact that the fusion hypotheses are nested within the larger hypotheses in the analysis. thus the poorer fit is a statistical artifact and not biologically meaningful. yet you are incorrectly interpreting a statistical artifact as as a lack of support for the fusion hypothesis.

==== I'm pointing out that the entire premise of your post is based on a faulty reading of the paper. THis paper does not say "...the fusion story is out and common descent is in." ====

I know the paper does not say this, but the results do.

==== when you say "But introducing the fusion event to create eukaryotes resulted in a poorer fit" you are exposing the source of your confusion. the poorer fit is caused by the fact that the fusion hypotheses are nested within the larger hypotheses in the analysis. thus the poorer fit is a statistical artifact and not biologically meaningful. ====

I think I see your confusion. Yes, the fusion models are a subset of the more general models, so the fits (not accounting for parsimony) cannot be as good. I was making a different point. The paper accounts for both fit quality and parsimony, and it finds that the fusion model for eukaryotes is inferior to the Class I UCA with no fusion.

Cornelius,"Newton's formulation held for a couple of centuries, and now for another century it still holds quite well for anything big enough to be seen." Except for the minor inconveniences of extra fast stars, the Pioneer anomaly, accelerating expansion, dark flow, extra energetic photons, etc that all are not explained or contradict Newton's formulations.

You've got pretty much everything backwards regarding the results from my analysis. My analysis does not test whether fusion hypotheses or strict tree-like evolution are better. The point is that UCA is the winner *regardless* of whether there was a fusion event or rampant HGT. In fact, the model selection scores clearly show that the Class II models (which include fusion scenarios) are the best. I did not directly address this issue, as it's not the point of the paper, and would require more sophisticated models to really nail down -- but if you read the supplementary material I show evidence from my data for the archaeal-bacterial fusion for the first eukaryote.

You also claim that "the entire analysis is based on sequence alignment scores", but that is incorrect. Have you read the methods?

Talk is cheap -- you can always criticize the models I used. But do the criticisms hold any water? The data speaks for itself, and the best models are the best models -- the model selection scores do not depend on my opinions, desires, or beliefs. The great thing about this methodology, is if you think you have a better model, with a well-defined likelihood function, that can explain the same sequence data, then you are of course able (and encouraged by me) to do the analysis, to throw it in the mix and see how it fares against the rest as judged by the model selection criteria.

Thank you for the response. I was beginning to see the problem. I've deleted the offending paragraph and will retract the entire entry after the comments die down. Please accept my apology for any false publicity this has created for you.

"but if you read the supplementary material I show evidence from my data for the archaeal-bacterial fusion for the first eukaryote."

There was no supplementary material available.

"You also claim that "the entire analysis is based on sequence alignment scores", but that is incorrect. Have you read the methods?"

I didn't mean every criteria used in the paper hinges on sequence alignments. I merely meant that without them you'd have no paper. Your statement that "Here I report tests of the theory of UCA using model selection theory, without assuming that sequence similarity indicates a genealogical relationship" would likely lead an objective reader to think that your analysis somehow confirms CD without using sequence alignments as evidence for genealogical relationship, which would be a false impression. I'm not sure I could think of a more misleading way to put it.

"Talk is cheap -- you can always criticize the models I used. But do the criticisms hold any water? The data speaks for itself, and the best models are the best models -- the model selection scores do not depend on my opinions, desires, or beliefs."

The scores themselves of course merely pop out of the computer. There certainly is no "opinions, desires, or beliefs" in the algorithm. But you are fooling yourself to think it stops there. You wrote in the paper:

"by statistical convention a score difference of 5 or greater is viewed as very strong empirical evidence for the hypothesis with the better score (in this work higher scores are better)."

That is, of course, false. One hypothesis comparing well against others does not translate into "very strong empirical evidence for the hypothesis." This is yet another example of the rationalism that underwrites evolutionary thought and has infected science. It is a well known problem but evolutionists and journals continue to propagate this misinformation. It then leads to the popular pieces such as the ScienceDaily piece I cited:

http://www.sciencedaily.com/releases/2010/05/100512131513.htm

which proclaims: "First Large-Scale Formal Quantitative Test Confirms Darwin's Theory of Universal Common Ancestry." Again this is of course false, but I doubt you're apprising them of the error. From there it infects everything from mainstream journalism and popular science periodicals to textbooks, academia, etc.

In your work you have promoted misinformation about evolution. But of course you've already been warned of that. At some point, it goes beyond a mere mistake, and you are well beyond that point. You are no longer merely making mistakes, and in your position the cost would be too great to retract.

One who promotes misinformation is, ultimately, a misinformer. One can hardly blame the *Science News* writers, the newspaper journalists, the non life scientists, the educators, the policy makers, etc., for believing evolution is a fact. They are just consumers of the misinformation. But the misinformation comes from somewhere.

So after you put up that little note about "This blog is erroneous and I will retract it. Apologies for the false publicity.", you declare Theobald to be an out-and-out liar. Stay classy, Corny-baby! Stay classy!

I believe that key sentence in Dr. Theobald's comment is "The great thing about this methodology, is if you think you have a better model, with a well-defined likelihood function, that can explain the same sequence data, then you are of course able (and encouraged by me) to do the analysis, to throw it in the mix and see how it fares against the rest as judged by the model selection criteria."

It is one thing to toss around the accusation of spreading misinformation. It is altogether something different to conclusively demonstrate it. Are you prepared to present your model? Do you even have a model?

For a minute after I saw the retraction I thought you were showing more class that Everyone at the Discovery Institute put together. Then I read your bitter whine. Thanks for bringing me back to reality.

I'm sure as a former biologist you are aware that dishonesty is the worst transgression that can be committed by a scientist. People lose their jobs and are excommunicated for life. We don't take accusations of dishonesty lightly. Either back them up or retract your last comment and apologize (again).

Alvy Singer: He can give it... do you have to give it so loud? I mean, aren't you ashamed to pontificate like that? And the funny part of it is, Marshall McLuhan, you don't know anything about Marshall McLuhan!

Man in Theatre Line: Oh, really? Well, it just so happens I teach a class at Columbia called "TV, Media and Culture." So I think my insights into Mr. McLuhan, well, have a great deal of validity!

Alvy Singer: Oh, do ya? Well, that's funny, because I happen to have Mr. McLuhan right here, so, so, yeah, just let me... [pulls McLuhan out from behind a nearby poster]

Alvy Singer: come over here for a second... tell him!

Marshall McLuhan: I heard what you were saying! You know nothing of my work! You mean my whole fallacy is wrong. How you got to teach a course in anything is totally amazing!

You deserve credit for doing the right thing and retracting the blog post, which was based on a misunderstanding, whether it was your fault or not. I wonder if Dr Theobald will do the right thing and write the editors of Science Daily etc. for their similar promulgation of misunderstanding about his paper, as he has written you.

Also, in the time between now and when you delete this blog post, it would be helpful to say a little more at the top -- a sentence or two about which aspect of the post was incorrect, and the fact that it was based on a misunderstanding of Theobald's paper. That would help readers sort out just how much of the thesis you are retracting (e.g. you presumably aren't retracting the part about the "certainties" of evolution changing frequently) without having to slog through all of the comments.

sez dr. theobald: "but if you read the supplementary material I show evidence from my data for the archaeal-bacterial fusion for the first eukaryote."sez corny: "There was no supplementary material available."Oh, really? Now, I'm just an ignorant layman, but when I look at the Naturewebpage which presents Dr. Theobald's letter titled "A formal test of the theory of universal common ancestry", one of the things I see just below, and to the right of, the title is a set of links called "article links". The link labeled "supplementary info" is broken, unfortunately, but the link labeled "Editor's summary" brings up a page which has a very unbroken link labeled "Supplementary information".Since you explicitly asserted that "There was no supplementary material available", and apparently feel that one broken link is sufficient grounds on which to launch an accusation of fraud -- and you know damned well that you have accused Dr. Theobald of fraud, even if you prefer to employ other specific words such as "misinformer" -- I have one question for you, Corny:Are you incompetent, or just lying?

Thanks for the admission of error and the promised retraction -- that's admirable.

There is indeed (extensive) supplementary material for the paper, and it is linked to in several places, most notably at the bottom of the full text (http://www.nature.com/nature/journal/v465/n7295/full/nature09014.html#/).

"I didn't mean every criteria used in the paper hinges on sequence alignments. I merely meant that without them you'd have no paper. Your statement that 'Here I report tests of the theory of UCA using model selection theory, without assuming that sequence similarity indicates a genealogical relationship' would likely lead an objective reader to think that your analysis somehow confirms CD without using sequence alignments as evidence for genealogical relationship, which would be a false impression. I'm not sure I could think of a more misleading way to put it."

There's a basic confusion here about my methodology. I obviously do use sequence alignments, but the analysis does not assume that there is a single sequence alignment for all life. Similarly, I use phylogenetic methods, but my analysis does not assume that there is a single phylogeny for all life. What do you have against sequence alignments anyway? Even the most radical YEC accepts them, for instance, for aligning homologous proteins like human polymorphisms, or, say, for aligning the homologous cytochrome c proteins of bacteria. The key point to understand is that my multiple ancestry models used a *different* sequence alignment for each set of taxa hypothesized to share common ancestry. Then the model selection tests decide which hypothesis is best. It is possible, for instance, that the model selection criteria could have chosen the hypothesis in which human proteins were in their own alignment, separate from the rest of life. But they didn't.

You then wrote:

"You [Douglas] wrote in the paper:

'by statistical convention a score difference of 5 or greater is viewed as very strong empirical evidence for the hypothesis with the better score (in this work higher scores are better).'

That is, of course, false. One hypothesis comparing well against others does not translate into 'very strong empirical evidence for the hypothesis.'"

Here I actually have no idea what you mean. It is quite true that, by statistical convention, a score difference of 5 or greater is viewed as very strong empirical evidence for the hypothesis with the better score. This is a statement I firmly stand by, and no scientist or statistician will find it controversial. Now perhaps you just don't like statistics. If so, then here the argument stops, because of course my analysis is fundamentally based on modern, cutting edge statistical methods. Pretty much all of science, however, believes that statistics is a necessary component of the scientific method -- it's really the only way to deal with uncertainty and noise in data.

You then write:

"This is yet another example of the rationalism that underwrites evolutionary thought and has infected science."

I'ts hard to imagine what you could mean by this, but you appear to think that science is wrong for being rational. But science is clearly fundamentally, and unapologetically, based on using reason. Again, it appears the argument ends here, as they say: you can't reason a man out of a position he didn't reason himself into.

One final comment about sequence alignments, to reiterate a point made earlier:

If you really don't like sequence alignments, then you, or anyone else, are perfectly capable (and highly encouraged by me) to develop your own model for the origin of these protein sequences that avoids using sequence alignments. Again, if you can specify the model in a detailed enough manner to calculate a likelihood for your hypothesis based on the observed data, you can trivially calculate its model selection score and see how it fares. That's the beauty of this methodology, and of science in general -- if you don't like my hypothesis you can just offer your own to explain the same data. There happens to be an objective way to determine which is the best.

====There's a basic confusion here about my methodology. I obviously do use sequence alignments, but the analysis does not assume that there is a single sequence alignment for all life. Similarly, I use phylogenetic methods, but my analysis does not assume that there is a single phylogeny for all life.====

No, there was no confusion about that.

====What do you have against sequence alignments anyway?====

Nothing. I was responding to your concern about my characterization of the role of sequence alignment scores in your method. My point was that sequence alignments, and the use of them as evidence for genealogical relationship, play an important role in the paper. Therefore, your statement: "Here I report tests of the theory of UCA using model selection theory, without assuming that sequence similarity indicates a genealogical relationship" is misleading. My point was not that you assume a single alignment or phylogeny for all life, but rather that your claim that you do not assume that "sequence similarity indicates a genealogical relationship" is misleading.

====Even the most radical YEC accepts them,====

Hmmm, maybe I should reject sequence alignments then ...

====The key point to understand is that my multiple ancestry models used a *different* sequence alignment for each set of taxa hypothesized to share common ancestry. Then the model selection tests decide which hypothesis is best. It is possible, for instance, that the model selection criteria could have chosen the hypothesis in which human proteins were in their own alignment, separate from the rest of life. But they didn't.====

Yes, agreed.

=============----You then write:

"You [Douglas] wrote in the paper:

'by statistical convention a score difference of 5 or greater is viewed as very strong empirical evidence for the hypothesis with the better score (in this work higher scores are better).'

That is, of course, false. One hypothesis comparing well against others does not translate into 'very strong empirical evidence for the hypothesis.'"----

=====It is quite true that, by statistical convention, a score difference of 5 or greater is viewed as very strong empirical evidence for the hypothesis with the better score.=====

Sure, such score differences are *viewed as* very strong empirical evidence by evolutionists. But such score differences are uncontroversially *not* "very strong empirical evidence for the hypothesis with the better score." Regardless of claims by evolutionists to the contrary.

=====This is a statement I firmly stand by, and no scientist or statistician will find it controversial. =====

Yes, evolutionists always do firmly stand by such statements. But it is exactly the opposite: no scientist or statistician would rightly ever make such a claim.

When comparing such scores a scientist or a statistician would merely claim that the hypothesis with the significantly higher score is the winner of the group. The hypothesis with the significantly higher score is clearly superior to the others, and wins *relative to* the others.

That is entirely different than your claim that the results constitute "very strong empirical evidence for the hypothesis." That is simply false. Such contrastive thinking is fallacious, yet it is fundamental in evolutionary thought. As I mentioned, this leads to reporting such as here:

http://www.sciencedaily.com/releases/2010/05/100512131513.htm

This ScienceDaily piece gives the misleading message that "First Large-Scale Formal Quantitative Test Confirms Darwin's Theory of Universal Common Ancestry." There was, of course, no such confirmation, but that is the natural conclusion from reading your paper. Yes, Universal Common Ancestry was confirmed as the winner from a set of alternatives, but that is a different claim.

====Now perhaps you just don't like statistics. If so, then here the argument stops, because of course my analysis is fundamentally based on modern, cutting edge statistical methods. =====

It's not the statistical methods that are the problem here.

===================You then write:

"This is yet another example of the rationalism that underwrites evolutionary thought and has infected science."

I'ts hard to imagine what you could mean by this, but you appear to think that science is wrong for being rational. But science is clearly fundamentally, and unapologetically, based on using reason. ===================

You're confusing rationalism with rational thought. Two different things. Your approach, and evolutionary thought in general, are deeply rationalistic. That is not to say evolutionary thought is rational (though usually it is). If you would like I could explain more.

"My point was that sequence alignments, and the use of them as evidence for genealogical relationship, play an important role in the paper. Therefore, your statement: 'Here I report tests of the theory of UCA using model selection theory, without assuming that sequence similarity indicates a genealogical relationship' is misleading."

The simple use of a sequence alignment does not imply that I am assuming that similarity indicates a genealogical relationship. My statement is true, and demonstrably so. Just because you can make a sequence alignment does not mean that the sequences are related, or even similar. And even if they are similar, that does not guarantee that the model selection scores will indicate common ancestry for those sequences. I give three examples in the supp matt of exactly this. QED.

Rather, what my reported test do, is evaluate the hypothesis that the sequences in an alignment are related by common ancestry, and nowhere in the models is it assumed that similarity implies common ancestry.

Nice of you to comment here, even after being called a career misinformer.

I was curious about Dr. Hunter's take on rationalism. Although I didn't read his book, a friendly review from a creationist website was illuminating. I quote them later. Dr. Hunter should correct the review if it is wrong. In short, he argues evolution is 'rationalist' because it rationalizes all data in terms of evolution, and forces data to fit the hypothesis, ignoring data to the contrary. Scientists are, therefore, either blindly mistaken or liars, and 'career misinformers'. ID then claims the high ground as the Tabula rasa alternative that has no presuppositions (no, I'm not kidding!).

http://creation.com/review-cornelius-hunter-sciences-blind-spot

"Francis Bacon stood for empiricism. His philosophical opponents were the Aristotelians who force-fit science into their ‘preconceived notions of how nature works’..... Science should be empiricism unrestrained, and it should be limited to subjects suitable for empirical research."

"Hunter’s focus is demonstrating that Darwinism has a host of empirical problems. And yet, because Darwinism is rationalistic, it refuses to acknowledge any of them."

"So, what might a science look like that does not take rationalism for granted? In his final chapter, Hunter suggests that it would be a ‘moderate empiricism,’ in the tradition of Francis Bacon. It would be suspicious of a priori assumptions, cautious in putting forward theories until sufficient empirical data (experiments and observations) are collected, and never overly devoted to a particular theory (pp. 137–140)."

So, Hunter MUST argue that the evidence for evolution is strictly non-empirical, or force-fit into the preconceived mold of evolution.

This is why your work is a threat. As a directly empirical work, without presupposition, it can test any model. One could conceivably throw in a model for vertebrates as an independent 'tree of life' (via special creation or arrival by mother-ship) and presumably come up with a terribly low score.

I have argued on this blogs the direct empirical observations of evolution through population genomics also match Hunter's call for moderate empiricism. If all genes in an evolving and speciating population can be sequenced (or significantly sampled by SNPs, etc.), and the changes traced, and experimentally tested, and even reverted, what else is there? What theory is forced in saying evolution was observed?

"Sure, such score differences are *viewed as* very strong empirical evidence by evolutionists."

And they are also viewed that way by other scientists, statisticians, and probability theorists. Evolutionary biologists did not invent the model selection methods, or likelihood statistics, or Bayesian statistics, or their interpretations.

You wrote:

"When comparing such scores a scientist or a statistician would merely claim that the hypothesis with the significantly higher score is the winner of the group. The hypothesis with the significantly higher score is clearly superior to the others, and wins *relative to* the others.

That is entirely different than your claim that the results constitute 'very strong empirical evidence for the hypothesis.' That is simply false. "

And you are simply incorrect. From a model selection perspective, from a likelihood perspective, and from a Bayesian perspective, empirical evidence can *only* be evaluated relative to other hypotheses. That's all we have. No hypothesis can be evaluated in isolation -- such an idea is impossible and incoherent. This view is not from evolutionary biology -- this is the standard non-frequentist statistical view (and even most frequentists have the same view). I suggest reading some introductory books on likelihood and Bayesian statistics.

And, as an aside, the view that hypotheses can only be evaluated relative to others does not imply the erroneous idea that evidence against one hypothesis is equal evidence for another.

You wrote:

"You're confusing rationalism with rational thought."

Ah, so you meant philosophical rationalism. That is even stranger, since statistics, particularly likelihoodist and Bayesian statistics and model selection theory, are inferential methods. They are about as opposite from philosophical rationalism as can possibly be.

When you say you will "retract" this post, do you mean that you will publicly admit that you were wrong about it,or that you will delete all references to both it _and_ your subsequent disavowal of it?

I think your current bold admission is sufficient. It would be a shame and misleading if people following links from other blogs and private emails were to find a 404-"not found" error in place of an honest admission of error.

"When comparing such scores a scientist or a statistician would merely claim that the hypothesis with the significantly higher score is the winner of the group. The hypothesis with the significantly higher score is clearly superior to the others, and wins *relative to* the others.

That is entirely different than your claim that the results constitute 'very strong empirical evidence for the hypothesis. That is simply false. "

And you are simply incorrect. =================

Well, there you have it. (More below.)

=================From a model selection perspective, from a likelihood perspective, and from a Bayesian perspective, empirical evidence can *only* be evaluated relative to other hypotheses. That's all we have. No hypothesis can be evaluated in isolation -- such an idea is impossible and incoherent. This view is not from evolutionary biology -- this is the standard non-frequentist statistical view (and even most frequentists have the same view). I suggest reading some introductory books on likelihood and Bayesian statistics. =================

Wow, evolutionists never cease to amaze--the lengths to which they must go is incredible. It is always striking to see the certainty with which evolutionists promote their philosophies and metaphysics. You can see it in the 17th c., in 18th c., 19th c., 20th c. and 21st. It just keeps on coming. They impose their philosophies, as though they were facts, on the world. Their faulty logic is exceeded only by their boldness.

The fact of the matter is when one hypothesis beats out others you cannot make the claims you are making. What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming.

I realize my explaining this will not bring you out of your denial. And "denial" seems to be the right word as the fallacy is so obvious.

But your appeal to the limitations in your confirmation methods doesn't change the fact that you are making false claims, and celebrating them as valid findings. The fact that "That's all we have" hardly justifies the publishing and promotion of misinformation. The fact that "That's all we have" ought to serve to temper the claims, not exalt them.

But contrastive thinking has been at the heart of evolutionary thought for centuries. From Kant to Darwin, and on up, what has always been rather revealing is how evolutionists have presented their proofs as though they were objective, undeniable findings. It is always a bit shocking to see such bold claims made on such faulty logic.

=====When you say you will "retract" this post, do you mean that you will publicly admit that you were wrong about it,or that you will delete all references to both it _and_ your subsequent disavowal of it?

I think your current bold admission is sufficient. It would be a shame and misleading if people following links from other blogs and private emails were to find a 404-"not found" error in place of an honest admission of error.=====

You and others have made some good points. For now, the important thing is that the offending paragraph has been deleted.

As you've stated many times? Like, um, when? Certainly not in this post from last year:"There must be some extremely powerful and compelling scientific evidence for evolution to make it a fact as gravity is a fact. That is what one would think. But, surprisingly, there is no such evidence."

I'm not having much luck finding these "many times" in your other posts, either. For the majority, they might be charitably said to imply that you possibly think there is empirical evidence for evolution. This is the only one I've yet found that really qualifies:"Did you know that most of the evidence claimed for evolution is actually not evidence for evolution? That's right, remember the mountain of evidence that evolutionists say is supposed to make evolution a fact? Well most of it consists of biological findings that merely have been interpreted according to evolution."

But, honestly, it's just a little hard to believe didn't really mean "all of it" rather than "most of it", given the highly obvious antievolutionary axe you so dearly love to grind and grind and grind.

Especially given the lack of actual direct statements to the effect that there really is evidence for evolution. Other than the one you just made here in the comments, of course.

But there's an idea: they could all be in the comment! Well, I haven't read every last one, but so far, I'm again not having much in the way of luck. Certainly not in this one, for example, written in response to the commenter Zachriel:

"======We have strong evidence of Common Descent and mechanisms of descent with modification, including the evolution of complex structures.======

Is that your F5 or F6 key? In fact, we have evidence *against* evolution."

OK...hmmm. In your books? I haven't read any of those, so if they do indeed contain these "many times", mayhap you could provide some page numbers?

I'm also given to understand that you give talks from time to time, so that's another possibility. Maybe you mentioned it in that one with the thylacines?

OK, you know what? This'd be a whole lot easier if you could just tell us what exactly it is you consider to be evidence for evolution. Manually datamining your blog via Google is, honestly, something of a chore.

The fact of the matter is when one hypothesis beats out others you cannot make the claims you are making. What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming.

On the contrary, you can have both; they are not mutually exclusive concepts.

Take the case of heliocentrism: There is strong evidence for it. AND there is stronger evidence in its favor vs geocentrism.

Cornelius wrote: The fact of the matter is when one hypothesis beats out others you cannot make the claims you are making. What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming.

That is how science works, Cornelius. Theories make predictions, predictions are tested empirically. A theory that survives these tests wins. That's how general relativity was established: it beat out Newtonian gravity. There may be a better theory out there that would unite general relativity and quantum physics, but until then general relativity rules. Your complaint rings hollow.

"What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming."

Fine, so from my analysis we have overwhelming evidence that universal common ancestry beats out competing multiple independent ancestry hypotheses. If you don't consider that as evidence for universal common ancestry, then you are certainly entitled to that opinion. But the rest of us are not required to believe that your opinion makes any sense. Yours is a strange philosophy, to my mind, and I'm sure to most people who will read your words.

***************************

I recommend reading David Penny's comments on my paper, at the end of this piece:

"What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming."

Fine, so from my analysis we have overwhelming evidence that universal common ancestry beats out competing multiple independent ancestry hypotheses. If you don't consider that as evidence for universal common ancestry, then you are certainly entitled to that opinion. But the rest of us are not required to believe that your opinion makes any sense. Yours is a strange philosophy, to my mind, and I'm sure to most people who will read your words.

***************************

I recommend reading David Penny's comments on my paper, at the end of this piece:

Since George has disabled comments on his latest post, I'll reply here, not so much for George but for the others here.

George has made a very significant error in comparing my methodology to Bernoulli's. And the error is extremely ironic (and pretty darn funny, if you are a statistics geek like me).

The results in my paper are explicitly based on model selection theory, likelihoodist and Bayesian statistics -- *not* on classical frequentist null-hypothesis testing, which in fact I criticize in the main text of the paper and in the supplementary materials. Bernoulli's solar system argument, however, is a classic example of a null-hypothesis test -- it is often cited as the first one known.

The irony here, of course, is that I don't use Bernoulli's methods, for the very reason that disproving the null hypothesis is not evidence for your favored hypothesis. Bernoulli's argument was fallacious because all he did was show that the random hypothesis (the null hypothesis) did not explain the data well. That says nothing about Bernoulli's favored hypothesis of a single solar cause. So in this sense George is correct, that "disproving" the null hypothesis is not evidence for the other hypothesis.

But this criticism does not apply to Bayesian statistics (or to likelihoodist and model selection methods). There is a rich history in Bayesian statistics in criticizing null-hypothesis tests, for this very reason. Bayesians consider null-hypothesis tests to be illogical.

Bernoulli's error was that he never considered how well his favored hypothesis (a single solar cause) explains the data. Bernoulli's hypothesis could have even been worse than the null hypothesis, for all he knew.

And this is the strength of the Bayesian methods I used -- with these methods, you have to explicitly calculate how well *all* the hypotheses explain the data, not just the "null". In fact, in my methodology there is not even such a thing as a random null hypothesis.

=====George has made a very significant error in comparing my methodology to Bernoulli's. And the error is extremely ironic (and pretty darn funny, if you are a statistics geek like me).

The results in my paper are explicitly based on model selection theory, likelihoodist and Bayesian statistics -- *not* on classical frequentist null-hypothesis testing, which in fact I criticize in the main text of the paper and in the supplementary materials. Bernoulli's solar system argument, however, is a classic example of a null-hypothesis test -- it is often cited as the first one known.

The irony here, of course, is that I don't use Bernoulli's methods,=====

But of course I made no such point. The point is that you are using contrastive reasoning (a much more general point), and making unsupportable claims, as Bernoulli did.

Of course you are not using his specific approach. They had no such thing as Bayesianism, model selection and so forth. Even Bayes initial work was still half a century away.

Well, sure Cornelius. But of course, you somehow fail to explain ANY of that in your latest (at least you provided a passing mention, so that's something I guess), AND since it's mostly just "Bernoulli this" and "Bernoulli that", people could very easily get the wrong impression. You might say that, if they didn't already know better, they'd be misled by your post. Or, perhaps, misinformed?

BTW, still pretending you didn't call Dr. Theobald a liar, I see. Ever going to address THAT issue, Cornelius? Or can we just expect more blog posts slagging Bernoulli or whatever?

Also, if you please, what was the evidence for evolution that you do accept again, since you've supposedly claimed it exists "many times"?